Items Covered in this Edition:
IMPORTANT NOTE: Two research SGIs have had recent hardware failures and one other workstation had some files accidentally deleted. None of these machines had a current backup. The Research Group System Administrator is responsible for backups of the workstation in his/her research lab.
AutoDock is installed on several SGI workstations in the Department. The output of this program is a series of ligand structures that are "docked" in the binding pocket of a macromolecule. This is accomplished by performing a Monte Carlo simulation of a flexible ligand as it randomly fluctuates about a static macromolecule (the macromolecule is represented by a large 3D grid). This differs from "traditional" docking methods, where the user had to direct the ligand into the binding pocket. While this program is CPU-intensive, preliminary results in the MolViz Facility have shown it to be very informative. Several small "interface" programs have been written by the MolViz Facility staff to transfer structures between InsightII and AutoDock. MolViz AutoDock notes are also available.
A new CSD upgrade is being installed at UCS; our local CSD software will be upgraded soon after UCS returns this
software to us. InsightII version 4.0.0 just arrived and will be installed soon. PCMODEL for all versions of the IRIX
operating systems has been installed. A version of GMMX for all IRIXs will also be installed soon. Netscape version
3.0 is now available for SGI workstations, although the latest version of Netscape that is officially recommended by SGI
is version 2.02S. If you need an updated version of Netscape, contact the
MolViz Facility Staff.
Retired Software
The following software has become obsolete due to the popularity and features of Netscape. This software will no
longer be supported by the MolViz Staff:
If one or more of these capabilities is needed but it is missing from Netscape as configured in your account or on your
workstation, contact the MolViz Staff. These applications will soon be removed from all departmental SGIs; research
SGIs that use copies of these programs on the departmental servers will also lose access to these programs. The
MolViz Facility Staff recommends that you remove copies of these programs that reside on your local machine.
The StereoView Classroom
The StereoView Classroom (room A400) is a fully
operational projection system for SGI and PC (Windows 95), and VCR output. Output from a Macintosh can also be
arranged if you supply the computer. "Stereo-Ready" outputs can also be displayed in active 3D mode with CrystalEyes
LCD glasses. The newest feature of A400 is the ability to capture video & audio from the SGI onto a VCR tape or
transfer VCR tape or IU cable TV output to the SGI. Contact Bob Addleman
or Katherine Mann to schedule this
resource.
While this classroom is operational, the MolViz Facility staff needs your suggestions and comments to make this resource fully
compatible with your research and instructional needs. If you would like to comment upon the functionality of this
resource, please contact the MolViz Facility staff.
We have now implemented "automount" on all of the Departmental SGIs and most of the Research Group SGIs.
"Automounting" automatically mounts a remote file system only when a user executes an application requiring access to
a file on the remote file system. When the application is finished, the system detects the inactivity and automatically
unmounts the file system after a delay (currently 5 minutes). For example, users who have a home directory on a remote
system can log onto an SGI workstation and their home directory will be automounted and immediately available.
Automounting eliminates network traffic and system administration efforts when the SGI workstations are not being
used, and it is a popular feature used in many SGI networks throughout the world.
Automounting causes several minor changes. Most importantly, the path name of home directories that exist on remote
systems are prefaced with /ruser, and the path name of application directories that exist on remote systems are prefaced
with /remote. For example, if Rachel has a home directory on CHEMVGX (/chemvgx/people/rachel) and she logs onto
PCHEM01, her home directory on PCHEM01 is named /ruser/chemvgx/people/rachel. If Rachel starts InsightII (by
typing InsightII) on PCHEM01, she accesses /remote/saturn3/model/biosym/950/bin/insightII, the copy of InsightII on
our server SATURN.
Commands that access all file systems on the SGI workstation will access only file systems that are currently
automounted. For example, df will only list file systems that have been used within 5 minutes. Since most people use
these commands to access only file systems on which they are currently working (and are therefore automounted), this
should not cause problems.
The privilege to mount a remote file system is no different than with the previous hard mounting and is defined in the
/etc/exports file of the system on which the remote file system is physically installed. The remote file systems that can
be automounted onto the local workstation are listed in /etc/auto.ruser and /etc/auto.remote.
Maintaining links to remote file systems such that specifying /model has teh same effect as /remote/model, for example,
defeats the purpose of automounting and effectively re-establishes the hard mounts as they wre before. It is
recommended that any such links be removed and appropriate changes be made in any scripts (/etc/cshrc,
/etc/cshrc.local, etc.), support files (/etc/passwd, etc.), or other programs affected. Failure to follow this precaution
could result in your system becoming unstable, very sluggish, or even unbootable when a remote file system is down and
you have links to this file system.
If you are interested in purchasing a new SGI workstation, please contact
Upgrade to IRIX 6.2
IRIX 6.2 has been installed on pchem01, pchem06, stereo1, and selected research SGI workstations. It is available for
installation on SGI workstations that have a CPU labeled "R4000" or higher (type hinv to list your CPU type). Most
Indigo workstations have R3000 CPUs and cannot be upgraded. While there are no immediate and specific reasons to
upgrade your operating system, the MolViz Facility Staff recommends upgrading to IRIX 6.2 to stay concurrent with new state-of-
the-art features offered by SGI and other software vendors. IRIX 6.2 also requires less disk space than previous
operating systems.
Automounting Disks between SGI workstations
File systems (selected directories and files on a hard disk drive) on one SGI workstation can be shared, or "mounted", by
other SGI workstations. The standard mounting method keeps the files mounted all of the time. This requires a perfect
network and significant efforts by system administrators to maintain and guarantee that files are always mounted. To
make matters worse, rebooting your system while a remotely mounted drive is unavailable can cause your system to
hang or run sluggishly while it tries to establish the connection.
New Workstations offered by Silicon Graphics, Inc.
The Indigo, Indy, Indigo2, and Challenge workstations have been replaced by new types of workstations:
Why are these machines so inexpensive? There are several reasons, but the biggest reason is due to VOLUME
production of the processor chips. Since May 1996, both Nintendo and Sony have ordered over 12 million RISC-
based MIPS CPU chips to be used in their consumer game products. Production costs have decreased from $2000
to $30 per chip!